We present a tool for multi-omics data analysis that enables simultaneous visualization of up to four types of omics data on organism-scale metabolic network diagrams. The tool’s interactive web-based metabolic charts depict the metabolic reactions, pathways, and metabolites of a single organism as described in a metabolic pathway database for that organism; the charts are constructed using automated graphical layout algorithms. The multi-omics visualization facility paints each individual omics dataset onto a different “visual channel” of the metabolic-network diagram. For example, a transcriptomics dataset might be displayed by coloring the reaction arrows within the metabolic chart, while a companion proteomics dataset is displayed as reaction arrow thicknesses, and a complementary metabolomics dataset is displayed as metabolite node colors. Once the network diagrams are painted with omics data, semantic zooming provides more details within the diagram as the user zooms in. Datasets containing multiple time points can be displayed in an animated fashion. The tool will also graph data values for individual reactions or metabolites designated by the user. The user can interactively adjust the mapping from data value ranges to the displayed colors and thicknesses to provide more informative diagrams.

GSE37703: Differential analysis of HOXA1 in adult cells at isoform resolution by RNA-Seq' for quantification by Kallisto and differential abundance with Sleuth dataset used for the "Reproducible in-silico omics analyses across clouds and clusters" paper.

The AVATARS project aims to enhance crop improvement by utilizing advanced molecular omics analyses and high-throughput phenotyping. In order to address the challenges posed by the increasing volume and complexity of data, novel analysis tools and approaches are being developed. This interdisciplinary project focuses on the seed formation of Brassica napus, also known as rapeseed or canola, and investigates genetic and environmental influences on seed quality using ultra-high-throughput single seed analyses and deep learning methods. As an integral part of the project, plants of the German winter-type oilseed rape cultivar Express 617 were grown under controlled field-like conditions in the IPK PhenoSphere (2020-2021). Samples were taken at five distinct stages of seed development, from pre-storage to seed maturation, for temporally and spatially resolved multi-omics analysis. The present dataset includes gene expression data obtained by mRNA sequencing and mass spectrometry-based proteomics data. For the first stage (pre-storage), whole seeds were analysed. In the later four stages, developing seeds were dissected into four organs/tissues (SC = seed coat, IC = inner cotyledon, OC = outer cotyledon, and RA = radicle). By employing virtual and augmented reality, researchers can visualize and explore multidimensional data in innovative ways, making them more accessible and enabling more efficient analyses. The project involves academic and industrial partners with expertise in various fields, collaborating to tackle these challenges and integrate data from multiple sources. By developing a time-resolved 3D seed model and utilizing advanced technologies, such as high-resolution MRI and histological data, the project will map complex omics datasets onto gene regulatory and metabolic networks for detailed analyses and intuitive visualization. The acquired datasets were deposited in central infrastructure of EMBL-EBI (ArrayExpress and PRIDE), facilitating efficient access and integration with other large datasets.

Studies on aging have largely included one or two OMICS layers, which may not necessarily reflect the signatures of other layers. Moreover, most aging studies have often compared very young (4-5 wks) mice with old (24 months) mice which does not reflect the aging transition after the attainment of adulthood. Therefore, we aimed to study and compared muti-OMICS aging signatures across key metabolic tissues of mature adults (6 months) and old (24 months) C57BL/6J mice (the most commonly used mouse strain). Here we compared the differentially regulated genes and enriched pathways for transcriptome, proteome and epigenome (H3K27ac, H3K4me3, H3K27me3, DNA methylation) across liver, heart, and quadriceps muscle. The major aging associated pathways cross multiple layers and tissues are decreased RNA metabolism, transcription, and translation at transcript and protein levels however increased potential of transcription at DNA methylation and H3K27ac levels.

Mangroves are dominant flora of intertidal zones along tropical and subtropical coastline around the world that offer important ecological and economic value. Recently, the genomes of mangroves have been decoded, and massive omics data were generated and deposited in the public databases. Reanalysis of multi-omics data can provide new biological insights excluded in the original studies. However, the requirements for computational resource and lack of bioinformatics skill for experimental researchers limit the effective use of the original data. To fill this gap, we uniformly processed 942 transcriptome data, 386 whole-genome sequencing data, and provided 13 reference genomes and 40 reference transcriptomes for 53 mangroves. Finally, we built an interactive web-based database platform MangroveDB (https://github.com/Jasonxu0109/MangroveDB), which was designed to provide comprehensive gene expression datasets to facilitate their exploration and equipped with several online analysis tools, including principal components analysis, differential gene expression analysis, tissue-specific gene expression analysis, GO and KEGG enrichment analysis. MangroveDB not only provides query functions about genes annotation, but also supports some useful visualization functions for analysis results, such as volcano plot, heatmap, dotplot, PCA plot, bubble plot, population structure etc. In conclusion, MangroveDB is a valuable resource for the mangroves research community to efficiently use the massive public omics datasets.

The Multiomics Market offers a range of products, including instruments, consumables, software, and services. Instruments include sequencing systems, mass spectrometers, and flow cytometers. Consumables encompass reagents, kits, and microarrays. Software solutions provide data analysis and visualization capabilities. Services include sample preparation, data analysis, and interpretation. Recent developments include: September 2023: The chromium single-cell gene expression flex assay manufactured by 10x Genomics Inc. now offers high throughput multi-omic cellular profiling as a commercially available capability thanks to the introduction of a new kit. Researchers and their options may detect simultaneous gene and protein expression, which can be expanded at a greater scale thanks to the new kit, which makes the multi-omic characterization of cell populations simple and efficient. The company's product portfolio was able to grow due to this technique., February 2023: Becton, Dickinson, and Company introduced the Rhapsody HT Xpress System, a high-throughput single-cell multiomics platform, to broaden the field of scientific research. With up to eight times more cells per sample than previous BD single-cell analyzers, this innovative technology allows scientists to extract, label, and analyze individual cells at a high sample throughput. This plan should assist the business in expanding its product's uses and serving more clients.. Notable trends are: Rising integration of multi-omics data is driving the market growth.

The Spatial OMICS Market Report is Segmented by Technology (Spatial Transcriptomics, Spatial Genomics, and Spatial Proteomics), Products (Instruments, Consumables, and Software), Sample ( Formalin-Fixed Paraffin-Embedded (FFPE), and Fresh Frozen), Application (Diagnostics, Translation Research, Drug Discovery and Development, Single Cell Analysis, Cell Biology, and Others), End User (Academic & Translational Research Institutes, Pharmaceutical & Biotechnology Companies, and Others), and Geography (North America, Europe, Asia-Pacific, and Rest of the World). The Report Offers Market Size and Forecasts for all the Above Segments in Value (USD).

Spatial OMICS market was valued at USD 226.32 million in 2020 and is expected to grow at a CAGR of 10.5% 2021 - 2028

Embryonic stem cells (ESCs) consist of a population of self-renewing cells displaying extensive phenotypic and functional heterogeneity. Research towards the understanding of the epigenetic mechanisms underlying the heterogeneity among ESCs is still in its initial stage. Key issues, such as how to identify cell-subset specifically methylated loci and how to interpret the biological meanings of methylation variations remain largely unexplored. To fill in the research gap, we implemented a computational pipeline to analyze single-cell methylome and to perform an integrative analysis with single-cell transcriptome data. According to the origins of variation in DNA methylation, we determined the genomic loci associated with allelic-specific methylation or asymmetric DNA methylation, and explored a beta mixture model to infer the genomic loci exhibiting cell-subset specific methylation (CSM). We observed that the putative CSM loci in ESCs are significantly enriched in CpG island (CGI) shelves and regions with histone marks for promoter and enhancer, and the genes hosting putative CSM loci show wide-ranging expression among ESCs. More interestingly, the putative CSM loci may be clustered into co-methylated modules enriching the binding motifs of distinct sets of transcription factors. Taken together, our study provided a novel tool to explore single-cell methylome and transcriptome to reveal the underlying transcriptional regulatory networks associated with epigenetic heterogeneity of ESCs.

The global single-cell omics market is estimated to grow from USD 3.89 billion in 2025 to USD 17.01 billion by 2035, representing a CAGR of 15.90%.

## GMarsGT: Multi-omics data analysis for rare population inference using single-cell graph transformer obtained from a mouse model for XYZ disease. The data was derived from 3 experimental groups: a control group (n=10), a disease group (n=10), and a treatment group (n=10).

## Data Collection The data was collected using GEO Database.

## Data Format The data is stored as TSV file and MTX file where each row represents a gene and each column represents a sample.

## Variables - Gene IDs: Gene Symbols (e.g., MALAT1) - Sample IDs: Sample identifiers (e.g., AAACATGCAAATTCGT-1) - Expression level: Row gene expression level.

Market Overview: The global single-cell omics market is burgeoning, with a market size of USD xx million in 2025 and a projected CAGR of xx% over the forecast period (2025-2033). Increasing government funding for genomics research, advancements in sequencing technologies, and rising demand for personalized medicine are the primary drivers of this market. However, factors such as high instrumentation costs and data analysis challenges may pose restraints. Geographically, North America dominates the market, followed by Europe and Asia-Pacific. Market Segmentation and Key Players: The single-cell omics market is segmented by application (drug discovery, disease diagnostics, biomarker discovery, and others) and type (single-cell RNA sequencing, single-cell proteomics, and single-cell genomics). Leading companies in the market include ANGLE Plc, BD, Bio-Rad Laboratories, Inc., Biognosys, CELLENION, CYTENA GmbH, Danaher Corporation, Illumina, Inc., Mission Bio, PerkinElmer Inc., Standard BioTools Inc., Vizgen, and 10x Genomics. These companies offer innovative solutions for single-cell analysis, contributing to the market's growth and expansion.

Duchenne muscular dystrophy (DMD) is a classical monogenic disorder, a model disease for genomic studies and a priority candidate for regenerative medicine and gene therapy. Although the genetic cause of DMD is well known, the molecular pathogenesis of disease and the response to therapy are incompletely understood. Here,we describe analyses of protein, mRNA and microRNA expression in the tibialis anterior of the mdx mouse model of DMD. Notably, 3272 proteins were quantifiable and 525 identified as differentially expressed in mdx muscle (P < 0.01). Therapeutic restoration of dystrophin by exon skipping induced widespread shifts in protein and mRNA expression towards wild-type expression levels, whereas the miRNome was largely unaffected. Comparison analyses between datasets showed that protein and mRNA ratios were only weakly correlated (r = 0.405), and identified a multitude of differentially affected cellular pathways, upstream regulators and predicted miRNA–target interactions. This study provides fundamental new insights into gene expression and regulation in dystrophic muscle. 3 Wt, 4 mdx and 4 Pip6e-PMO treated mdx mice

Acetyl-CoA is a key metabolite in all organisms, implicated in transcriptional regulation, post-translational modification as well as fuelling the TCA-cycle and the synthesis and elongation of fatty acids (FAs). The obligate intracellular parasite Toxoplasma gondii possesses two enzymes which produce acetyl-CoA in the cytosol and nucleus: acetyl-CoA synthetase (ACS) and ATP-citrate lyase (ACL), while the branched-chain α-keto acid dehydrogenase-complex (BCKDH) generates acetyl-CoA in the mitochondrion. To obtain a global and integrative picture of the role of distinct sub-cellular acetyl-CoA pools, we measured the acetylome, transcriptome, proteome and metabolome of parasites lacking ACL/ACS or BCKDH. Loss of ACL/ACS results in the hypo-acetylation of nucleo-cytosolic and secretory proteins, alters gene expression broadly and is required for the synthesis of parasite-specific FAs. In contrast, loss of BCKDH causes few specific changes in the acetylome, transcriptome and proteome which allow these parasites to rewire their metabolism to adapt to the obstruction of the TCA-cycle.

Single-cell multi-omics market is projected to reach $7.72 billion by 2033 from $1.43 billion in 2022, growing at a CAGR of 17.27% during the forecast period 2023-2033.

Global omics lab services market size is expected to reach USD 245.69 billion by 2032 at a CAGR of 13.4%, according to a new study by Polaris market research.

The Single Cell Multi Omics Market offers a range of products and services to meet the diverse needs of researchers. These include:Single-Cell Genomics: Technologies for sequencing and analyzing the DNA and RNA of individual cells.Single-Cell Proteomics: Technologies for identifying and quantifying proteins within individual cells.Single-Cell Metabolomics: Technologies for studying the metabolic activity of individual cells.Single-Cell Transcriptomics: Technologies for analyzing the RNA transcripts of individual cells. Recent developments include: October 2022: Innovation life science reagent and device firms Takara Bio USA, Inc. and BioExcel Diagnostic tools are developing and verifying a high-level, comprehensive technique for diagnosing infectious diseases based on syndromic markers. A fully owned subsidiary of Takara Bio Inc. is Takara Bio USA, Inc., September 2022: QIAGEN and Neuron23 Inc., the first biotechnology company devoted to creating precision drugs for based on genetic neurological and immunological disorders, declared the signing of an agreement to develop a partner screening for Neuron23's brain penetrant, blocker for Parkinson's disease., March 2023: Bio-Rad was given the iQ-Check kits that the company sells are approved by AOAC International and AFNOR for use with the CFX Opus Deep well Real-time PCR System.. Notable trends are: The growing adoption of sustainable environmental solutions is driving the market growth..

In this project, we developed a data resource based on the German winter oilseed rape cultivar Express 617. Plants were grown under controlled environmental conditions in the container-based system of the IPK PhenoSphere in 2020-2021. The dataset comprises gene expression data generated by RNA sequencing of different seed tissues across five stages of seed development, spanning early embryo/seed development, seed filling, and seed maturation. In the first stage (pre-storage), whole seeds were analysed. In the later four stages, developing seeds were dissected into four organs/tissues (SC = seed coat, IC = inner cotyledon, OC = outer cotyledon, and RA = radicle). This dataset (mRNA sequencing) is part of a series of multi-omics data generated in the frame of the AVATARS project.

Given the limited knowledge of the biological impact of spaceflight a multi-omics systems biology approach was used to investigate NASA xe2 x80 x99s GeneLab data and astronaut biomedical profiles. These data consist of hundreds of samples flown in space human metrics from 59 astronauts and confirmatory data from NASA xe2 x80 x99s Twin Study analyzed together for consistent transcriptomic proteomic metabolomic and epigenetic response to spaceflight. Pathway analysis showed significant enrichment of mitochondrial activity and innate immunity. Muscle and liver tissues showed that chronic inflammation may be a response to mitochondrial dysfunction. Additional pathways altered in spaceflight included cell cycle circadian rhythm and olfactory activity pathways all of which are known to have interactions with mitochondrial activity. Evidence of altered mitochondrial function was also found in the urine and blood metabolic data compiled from the astronaut cohort and NASA Twin Study data all of which indicate mitochondrial stress as a consistent phenotype of spaceflight.

Mycobacterium tuberculosis Beijing B0/W148 is one of the most widely distributed clusters in the Russian Federation and in some countries of the former Soviet Union. Recent studies have improved our understanding of the reasons for the “success” of the cluster but this area remains incompletely studied. Here, we focused on the system omics analysis of the RUS_B0 strain belonging to the Beijing B0/W148 cluster. Completed genome sequence of RUS_B0 (CP020093.1) and a collection of WGS for 200 cluster strains from the NCBI were used to describe the main genetic features of the population, as well as the level of resistance. In turn, proteome and transcriptome studies allowed to confirm the genomic data and to identify a number of finds that have not previously been described. Our results demonstrate that expression of the whiB6 which contains cluster-specific polymorphism (T4338371G) increased by more than 50 times in RUS_B0. Additionally, the level of ethA transcripts in RUS_B0 is increased almost 30 times compared to the H37Rv. Start sites for 10 genes were corrected based on the combination of proteomic and transcriptomic data. Additionally, based on the omics approach, we identified 5 new genes.